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Xiong S, Zhou J, Tan TK, Chung TH, Tan TZ, Toh SHM, Tang NXN, Jia Y, See YX, Fullwood MJ, Sanda T, Chng WJ. Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma. Nat Commun 2024; 15:6810. [PMID: 39122682 PMCID: PMC11316114 DOI: 10.1038/s41467-024-50910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Multiple myeloma is a hematological malignancy arising from immunoglobulin-secreting plasma cells. It remains poorly understood how chromatin rewiring of regulatory elements contributes to tumorigenesis and therapy resistance in myeloma. Here we generate a high-resolution contact map of myeloma-associated super-enhancers by integrating H3K27ac ChIP-seq and HiChIP from myeloma cell lines, patient-derived myeloma cells and normal plasma cells. Our comprehensive transcriptomic and phenomic analyses prioritize candidate genes with biological and clinical implications in myeloma. We show that myeloma cells frequently acquire SE that transcriptionally activate an oncogene PPP1R15B, which encodes a regulatory subunit of the holophosphatase complex that dephosphorylates translation initiation factor eIF2α. Epigenetic silencing or knockdown of PPP1R15B activates pro-apoptotic eIF2α-ATF4-CHOP pathway, while inhibiting protein synthesis and immunoglobulin production. Pharmacological inhibition of PPP1R15B using Raphin1 potentiates the anti-myeloma effect of bortezomib. Our study reveals that myeloma cells are vulnerable to perturbation of PPP1R15B-dependent protein homeostasis, highlighting a promising therapeutic strategy.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nicole Xin Ning Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Takaomi Sanda
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore.
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2
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Zhou B, Hu P, Liu G, Chang Z, Dong Z, Li Z, Yin Y, Tian Z, Han G, Wang W, Li X. Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements. Nat Commun 2024; 15:6303. [PMID: 39060230 PMCID: PMC11282110 DOI: 10.1038/s41467-024-50529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Chromosome rearrangements may distort 3D chromatin architectures and thus change gene regulation, yet how 3D chromatin structures evolve in insects is largely unknown. Here, we obtain chromosome-level genomes for four butterfly species, Graphium cloanthus, Graphium sarpedon, Graphium eurypylus with 2n = 30, 40, and 60, respectively, and Papilio bianor with 2n = 60. Together with large-scale Hi-C data, we find that inter-chromosome rearrangements very rarely disrupted the pre-existing 3D chromatin structure of ancestral chromosomes. However, some intra-chromosome rearrangements changed 3D chromatin structures compared to the ancestral configuration. We find that new TADs and subTADs have emerged across the rearrangement sites where their adjacent compartments exhibit uniform types. Two intra-chromosome rearrangements altered Rel and lft regulation, potentially contributing to wing patterning differentiation and host plant choice. Notably, butterflies exhibited chromatin loops between Hox gene cluster ANT-C and BX-C, unlike Drosophila. Our CRISPR-Cas9 experiments in butterflies confirm that knocking out the CTCF binding site of the loops in BX-C affected the phenotypes regulated by Antp in ANT-C, resulting in legless larva. Our results reveal evolutionary patterns of insect 3D chromatin structures and provide evidence that 3D chromatin structure changes can play important roles in the evolution of traits.
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Affiliation(s)
- Botong Zhou
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ping Hu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhou Chang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zihe Li
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yin
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, 621000, China
| | - Zunzhe Tian
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ge Han
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wen Wang
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China.
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
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Li J, Lin Y, Li D, He M, Kui H, Bai J, Chen Z, Gou Y, Zhang J, Wang T, Tang Q, Kong F, Jin L, Li M. Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305706. [PMID: 38582509 PMCID: PMC11200017 DOI: 10.1002/advs.202305706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Haplotype-resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high-resolution Hi-C diploid maps (1.2-kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post-hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi-scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent-of-origin-specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter-enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development-related genes are related to genetic variation between breeds, however, only a minority of breed-specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype-specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Diyan Li
- School of PharmacyChengdu UniversityChengdu610106China
| | - Mengnan He
- Wildlife Conservation Research DepartmentChengdu Research Base of Giant Panda BreedingChengdu610057China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Tao Wang
- School of PharmacyChengdu UniversityChengdu610106China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Fanli Kong
- College of Life ScienceSichuan Agricultural UniversityYa'an625014China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
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4
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Wang X, Yue F. Hijacked enhancer-promoter and silencer-promoter loops in cancer. Curr Opin Genet Dev 2024; 86:102199. [PMID: 38669773 DOI: 10.1016/j.gde.2024.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/19/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Recent work has shown that besides inducing fusion genes, structural variations (SVs) can also contribute to oncogenesis by disrupting the three-dimensional genome organization and dysregulating gene expression. At the chromatin-loop level, SVs can relocate enhancers or silencers from their original genomic loci to activate oncogenes or repress tumor suppressor genes. On a larger scale, different types of alterations in topologically associating domains (TADs) have been reported in cancer, such as TAD expansion, shuffling, and SV-induced neo-TADs. Furthermore, the transformation from normal cells to cancerous cells is usually coupled with active or repressive compartmental switches, and cancer-specific compartments have been proposed. This review discusses the sites, and the other latest advances in studying how SVs disrupt higher-order genome structure in cancer, which in turn leads to oncogene dysregulation. We also highlight the clinical implications of these changes and the challenges ahead in this field.
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Affiliation(s)
- Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai, China.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA.
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5
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Binder M, Szalat RE, Talluri S, Fulciniti M, Avet-Loiseau H, Parmigiani G, Samur MK, Munshi NC. Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes. Nat Commun 2024; 15:4139. [PMID: 38755155 PMCID: PMC11098817 DOI: 10.1038/s41467-024-47793-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.
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Affiliation(s)
- Moritz Binder
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Srikanth Talluri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | | | - Hervé Avet-Loiseau
- University Cancer Center of Toulouse, Institut National de la Santé, Toulouse, France
| | - Giovanni Parmigiani
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mehmet K Samur
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
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Yoon I, Kim U, Song Y, Park T, Lee DS. 3C methods in cancer research: recent advances and future prospects. Exp Mol Med 2024; 56:788-798. [PMID: 38658701 PMCID: PMC11059347 DOI: 10.1038/s12276-024-01236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
In recent years, Hi-C technology has revolutionized cancer research by elucidating the mystery of three-dimensional chromatin organization and its role in gene regulation. This paper explored the impact of Hi-C advancements on cancer research by delving into high-resolution techniques, such as chromatin loops, structural variants, haplotype phasing, and extrachromosomal DNA (ecDNA). Distant regulatory elements interact with their target genes through chromatin loops. Structural variants contribute to the development and progression of cancer. Haplotype phasing is crucial for understanding allele-specific genomic rearrangements and somatic clonal evolution in cancer. The role of ecDNA in driving oncogene amplification and drug resistance in cancer cells has also been revealed. These innovations offer a deeper understanding of cancer biology and the potential for personalized therapies. Despite these advancements, challenges, such as the accurate mapping of repetitive sequences and precise identification of structural variants, persist. Integrating Hi-C with multiomics data is key to overcoming these challenges and comprehensively understanding complex cancer genomes. Thus, Hi-C is a powerful tool for guiding precision medicine in cancer research and treatment.
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Affiliation(s)
- Insoo Yoon
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Uijin Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Yousuk Song
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Taesoo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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Choppavarapu L, Fang K, Liu T, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584872. [PMID: 38559097 PMCID: PMC10979939 DOI: 10.1101/2024.03.13.584872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Current knowledge in three-dimensional (3D) chromatin regulation in normal and disease states was mostly accumulated through Hi-C profiling in in vitro cell culture system. The limitations include failing to recapitulate disease-specific physiological properties and often lacking clinically relevant disease microenvironment. In this study, we conduct tissue-specific Hi-C profiling in a pilot cohort of 12 breast tissues comprising of two normal tissues (NTs) and ten ER+ breast tumor tissues (TTs) including five primary tumors (PTs), and five tamoxifen-treated recurrent tumors (RTs). We find largely preserved compartments, highly heterogeneous topological associated domains (TADs) and intensively variable chromatin loops among breast tumors, demonstrating 3D chromatin-regulated breast tumor heterogeneity. Further cross-examination identifies RT-specific looping-mediated biological pathways and suggests CA2, an enhancer-promoter looping (EPL)-mediated target gene within the bicarbonate transport metabolism pathway, might play a role in driving the tamoxifen resistance. Remarkably, the inhibition of CA2 not only impedes tumor growth both in vitro and in vivo , but also reverses chromatin looping. Our study thus yields significant mechanistic insights into the role and clinical relevance of 3D chromatin architecture in breast cancer endocrine resistance.
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8
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Yang Z, Shi M, Liang Y, Zhang F, Li C, Lu Y, Yin T, Wang Z, Li Y, Hao M, Guo R, Yang H, Lei G, Sun F, Zhang Y, Deng Z, Tian Y, Yu L, Bai C, Wang L, Wan C, Wang H, Yang P. Three-dimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus. J Gastroenterol 2024; 59:119-137. [PMID: 37925679 DOI: 10.1007/s00535-023-02053-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. METHODS Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. RESULTS: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4-chr10, chr13-chr21, chr15-chr22, and chr16-chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A-B or B-A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000-6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. CONCLUSION This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development.
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Affiliation(s)
- Zhao Yang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China.
| | - Mengran Shi
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Youfeng Liang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fuhan Zhang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Cong Li
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yinying Lu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Taian Yin
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhaohai Wang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yongchao Li
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Mingxuan Hao
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Rui Guo
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hao Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guanglin Lei
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Fang Sun
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Yu Zhang
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Zhuoya Deng
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuying Tian
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Linxiang Yu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Changqing Bai
- Department of Respiratory, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Lei Wang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chuanxing Wan
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Haifeng Wang
- Department of Urology, Second Affiliated Hospital of Kunming Medical University, Kunming, 650504, China.
| | - Penghui Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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9
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Li G, Pu P, Pan M, Weng X, Qiu S, Li Y, Abbas SJ, Zou L, Liu K, Wang Z, Shao Z, Jiang L, Wu W, Liu Y, Shao R, Liu F, Liu Y. Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer. Front Med 2024; 18:109-127. [PMID: 37721643 DOI: 10.1007/s11684-023-1008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/05/2023] [Indexed: 09/19/2023]
Abstract
Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial-mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer-promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.
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Affiliation(s)
- Guoqiang Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Peng Pu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Mengqiao Pan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Xiaoling Weng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Shimei Qiu
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200082, China
| | - Yiming Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Sk Jahir Abbas
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Lu Zou
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Ke Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Zheng Wang
- Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Ziyu Shao
- Department of General Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200082, China
| | - Lin Jiang
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
- Department of General Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200082, China
| | - Wenguang Wu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Yun Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
| | - Rong Shao
- Department of Pharmacology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Fatao Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
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10
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Gong L, Qiu L, Hao M. Novel Insights into the Initiation, Evolution, and Progression of Multiple Myeloma by Multi-Omics Investigation. Cancers (Basel) 2024; 16:498. [PMID: 38339250 PMCID: PMC10854875 DOI: 10.3390/cancers16030498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
The evolutionary history of multiple myeloma (MM) includes malignant transformation, followed by progression to pre-malignant stages and overt malignancy, ultimately leading to more aggressive and resistant forms. Over the past decade, large effort has been made to identify the potential therapeutic targets in MM. However, MM remains largely incurable. Most patients experience multiple relapses and inevitably become refractory to treatment. Tumor-initiating cell populations are the postulated population, leading to the recurrent relapses in many hematological malignancies. Clonal evolution of tumor cells in MM has been identified along with the disease progression. As a consequence of different responses to the treatment of heterogeneous MM cell clones, the more aggressive populations survive and evolve. In addition, the tumor microenvironment is a complex ecosystem which plays multifaceted roles in supporting tumor cell evolution. Emerging multi-omics research at single-cell resolution permits an integrative and comprehensive profiling of the tumor cells and microenvironment, deepening the understanding of biological features of MM. In this review, we intend to discuss the novel insights into tumor cell initiation, clonal evolution, drug resistance, and tumor microenvironment in MM, as revealed by emerging multi-omics investigations. These data suggest a promising strategy to unravel the pivotal mechanisms of MM progression and enable the improvement in treatment, both holistically and precisely.
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Affiliation(s)
- Lixin Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
- Gobroad Healthcare Group, Beijing 100072, China
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
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11
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Abstract
Lymphoid neoplasms represent a heterogeneous group of disease entities and subtypes with markedly different molecular and clinical features. Beyond genetic alterations, lymphoid tumors also show widespread epigenomic changes. These severely affect the levels and distribution of DNA methylation, histone modifications, chromatin accessibility, and three-dimensional genome interactions. DNA methylation stands out as a tracer of cell identity and memory, as B cell neoplasms show epigenetic imprints of their cellular origin and proliferative history, which can be quantified by an epigenetic mitotic clock. Chromatin-associated marks are informative to uncover altered regulatory regions and transcription factor networks contributing to the development of distinct lymphoid tumors. Tumor-intrinsic epigenetic and genetic aberrations cooperate and interact with microenvironmental cells to shape the transcriptome at different phases of lymphoma evolution, and intraclonal heterogeneity can now be characterized by single-cell profiling. Finally, epigenetics offers multiple clinical applications, including powerful diagnostic and prognostic biomarkers as well as therapeutic targets.
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Affiliation(s)
- Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
| | - José Ignacio Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
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12
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Lestringant V, Guermouche-Flament H, Jimenez-Pocquet M, Gaillard JB, Penther D. Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization. Curr Res Transl Med 2024; 72:103440. [PMID: 38447270 DOI: 10.1016/j.retram.2024.103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.
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Affiliation(s)
| | | | | | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France
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13
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Ding T, Zhang J, Xu H, Zhang X, Yang F, Shi Y, Bai Y, Yang J, Chen C, Zhang H. In-depth understanding of higher-order genome architecture in orphan cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188948. [PMID: 37394019 DOI: 10.1016/j.bbcan.2023.188948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
The human genome is intertwined, folded, condensed, and gradually constitutes the 3D architecture, thereby affecting transcription and widely involving in tumorigenesis. Incidence and mortality rates for orphan cancers increase due to poor early diagnosis and lack of effective medical treatments, which are now getting attention. In-depth understanding in tumorigenesis has fast-tracked over the last decade, however, the further role and mechanism of 3D genome organization in variant orphan tumorigenesis remains to be fully understood. We summarize for the first time that higher-order genome organization can provide novel insights into the occurrence mechanisms of orphan cancers, and discuss probable future research directions for drug development and anti-tumor therapies.
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Affiliation(s)
- Tianyi Ding
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Jixing Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Haowen Xu
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Xiaoyu Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Fan Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Yibing Shi
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Yiran Bai
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Jiaqi Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - Chaoqun Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China
| | - He Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai, PR China; Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an, Jiangxi province, PR China; School of Life Science, Jinggangshan University, Ji'an, Jiangxi province, PR China.
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14
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Song T, Yao M, Yang Y, Liu Z, Zhang L, Li W. Integrative Identification by Hi-C Revealed Distinct Advanced Structural Variations in Lung Adenocarcinoma Tissue. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:390-407. [PMID: 37589026 PMCID: PMC10425312 DOI: 10.1007/s43657-023-00103-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 08/18/2023]
Abstract
Advanced three-dimensional structure variations of chromatin in large genome fragments, such as conversion of A/B compartment, topologically associated domains (TADs) and chromatin loops are related closely to occurrence of malignant tumors. However, the structural characteristics of lung cancer still remain uncovered. In this study, we used high-throughput chromosome (Hi-C) conformation capture technology to detect the advanced structural variations in chromatin of two non-smoking lung adenocarcinoma (LUAD) tumor and paired normal tissues. The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues. At compartment scale, the main conversion type of compartment is A → B in tumor tissues, which are concentrated mainly on chromosome 3 (Chr3) (33.6%). A total of 216 tumor-specific TADs are identified in tumor tissues, which are distributed mainly in Chr1 (19), Chr2 (15) and Chr3 (17). Forty-one distinct enhancer-promoter loops are observed in tumor tissue, which are associated closely to tumor-related pathways including mitogen-activated protein kinase (MAPK), Phosphatidylinositol-3-kinase-Protein kinase B (PI3K-AKT), Ras, Wnt and Ras1. The most important observation in this study is that we identify five important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which are detected in both A → B compartment, TADs and chromatin loops in tumor samples, and four of these genes (NCEH1, NXPE3, MB21D2, and DZIP1L) locate on q arm of Chr3. Further gene expression and invasion experiment analysis show that NCEH1, MB21D2 and SYT16 are involved in the tumor development. Thus, we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.
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Affiliation(s)
- Tingting Song
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Menglin Yao
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Ying Yang
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Zhiqiang Liu
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Li Zhang
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
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15
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Kim Y, Yang H, Lee D. Cell line-specific features of 3D chromatin organization in hepatocellular carcinoma. Genomics Inform 2023; 21:e19. [PMID: 37704209 PMCID: PMC10326539 DOI: 10.5808/gi.23015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 07/08/2023] Open
Abstract
Liver cancer, particularly hepatocellular carcinoma (HCC), poses a significant global threat to human lives. To advance the development of innovative diagnostic and treatment approaches, it is essential to examine the hidden features of HCC, particularly its 3D genome architecture, which is not well understood. In this study, we investigated the 3D genome organization of four HCC cell lines-Hep3B, Huh1, Huh7, and SNU449-using in situ Hi-C and assay for transposase-accessible chromatin sequencing. Our findings revealed that HCC cell lines had more long-range interactions, both intra-and interchromosomal, compared to human mammary epithelial cells (HMECs). Unexpectedly, HCC cell lines displayed cell line-specific compartmental modifications at the megabase (Mb) scale, which could potentially be leveraged in determining HCC subtypes. At the sub-Mb scale, we observed decreases in intra-TAD (topologically associated domain) interactions and chromatin loops in HCC cell lines compared to HMECs. Lastly, we discovered a correlation between gene expression and the 3D chromatin architecture of SLC8A1, which encodes a sodium-calcium antiporter whose modulation is known to induce apoptosis by comparison between HCC cell lines and HMECs. Our findings suggest that HCC cell lines have a distinct 3D genome organization that is different from those of normal and other cancer cells based on the analysis of compartments, TADs, and chromatin loops. Overall, we take this as evidence that genome organization plays a crucial role in cancer phenotype determination. Further exploration of epigenetics in HCC will help us to better understand specific gene regulation mechanisms and uncover novel targets for cancer treatment.
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Affiliation(s)
- Yeonwoo Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyeokjun Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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16
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Nau A, Shen Y, Sanchorawala V, Prokaeva T, Morgan GJ. Complete variable domain sequences of monoclonal antibody light chains identified from untargeted RNA sequencing data. Front Immunol 2023; 14:1167235. [PMID: 37143670 PMCID: PMC10151772 DOI: 10.3389/fimmu.2023.1167235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction Monoclonal antibody light chain proteins secreted by clonal plasma cells cause tissue damage due to amyloid deposition and other mechanisms. The unique protein sequence associated with each case contributes to the diversity of clinical features observed in patients. Extensive work has characterized many light chains associated with multiple myeloma, light chain amyloidosis and other disorders, which we have collected in the publicly accessible database, AL-Base. However, light chain sequence diversity makes it difficult to determine the contribution of specific amino acid changes to pathology. Sequences of light chains associated with multiple myeloma provide a useful comparison to study mechanisms of light chain aggregation, but relatively few monoclonal sequences have been determined. Therefore, we sought to identify complete light chain sequences from existing high throughput sequencing data. Methods We developed a computational approach using the MiXCR suite of tools to extract complete rearranged IGVL-IGJL sequences from untargeted RNA sequencing data. This method was applied to whole-transcriptome RNA sequencing data from 766 newly diagnosed patients in the Multiple Myeloma Research Foundation CoMMpass study. Results Monoclonal IGVL-IGJL sequences were defined as those where >50% of assigned IGK or IGL reads from each sample mapped to a unique sequence. Clonal light chain sequences were identified in 705/766 samples from the CoMMpass study. Of these, 685 sequences covered the complete IGVL-IGJL region. The identity of the assigned sequences is consistent with their associated clinical data and with partial sequences previously determined from the same cohort of samples. Sequences have been deposited in AL-Base. Discussion Our method allows routine identification of clonal antibody sequences from RNA sequencing data collected for gene expression studies. The sequences identified represent, to our knowledge, the largest collection of multiple myeloma-associated light chains reported to date. This work substantially increases the number of monoclonal light chains known to be associated with non-amyloid plasma cell disorders and will facilitate studies of light chain pathology.
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Affiliation(s)
- Allison Nau
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
| | - Yun Shen
- Research Computing Services, Boston University, Boston, MA, United States
| | - Vaishali Sanchorawala
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
- Section of Hematology and Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
| | - Tatiana Prokaeva
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
| | - Gareth J. Morgan
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
- Section of Hematology and Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
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17
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Sanalkumar R, Dong R, Lee L, Xing YH, Iyer S, Letovanec I, La Rosa S, Finzi G, Musolino E, Papait R, Chebib I, Nielsen GP, Renella R, Cote GM, Choy E, Aryee M, Stegmaier K, Stamenkovic I, Rivera MN, Riggi N. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. SCIENCE ADVANCES 2023; 9:eabo3789. [PMID: 37000878 DOI: 10.1126/sciadv.abo3789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 01/18/2023] [Indexed: 06/19/2023]
Abstract
Cell fate transitions observed in embryonic development involve changes in three-dimensional genomic organization that provide proper lineage specification. Whether similar events occur within tumor cells and contribute to cancer evolution remains largely unexplored. We modeled this process in the pediatric cancer Ewing sarcoma and investigated high-resolution looping and large-scale nuclear conformation changes associated with the oncogenic fusion protein EWS-FLI1. We show that chromatin interactions in tumor cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Conversely, EWS-FLI1 depletion led to the disassembly of these looping networks and a widespread nuclear reorganization through the establishment of new looping patterns and large-scale compartment configuration matching those observed in mesenchymal stem cells, a candidate Ewing sarcoma progenitor. Our data demonstrate that major architectural features of nuclear organization in cancer cells can depend on single oncogenes and are readily reversed to reestablish latent differentiation programs.
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Affiliation(s)
- Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefano La Rosa
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- IRCSS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ivan Chebib
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Aryee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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18
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Li J, Gao L, Ye Y. HiSV: A control-free method for structural variation detection from Hi-C data. PLoS Comput Biol 2023; 19:e1010760. [PMID: 36608109 DOI: 10.1371/journal.pcbi.1010760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/24/2022] [Indexed: 01/07/2023] Open
Abstract
Structural variations (SVs) play an essential role in the evolution of human genomes and are associated with cancer genetics and rare disease. High-throughput chromosome capture (Hi-C) technology probed all genome-wide crosslinked chromatin to study the spatial architecture of chromosomes. Hi-C read pairs can span megabases, making the technology useful for detecting large-scale SVs. So far, the identification of SVs from Hi-C data is still in the early stages with only a few methods available. Especially, no algorithm has been developed that can detect SVs without control samples. Therefore, we developed HiSV (Hi-C for Structural Variation), a control-free method for identifying large-scale SVs from a Hi-C sample. Inspired by the single image saliency detection model, HiSV constructed a saliency map of interaction frequencies and extracted saliency segments as large-scale SVs. By evaluating both simulated and real data, HiSV not only detected all variant types, but also achieved a higher level of accuracy and sensitivity than existing methods. Moreover, our results on cancer cell lines showed that HiSV effectively detected eight complex SV events and identified two novel SVs of key factors associated with cancer development. Finally, we found that integrating the result of HiSV helped the WGS method to identify a total number of 94 novel SVs in two cancer cell lines.
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Affiliation(s)
- Junping Li
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Lin Gao
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Yusen Ye
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
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19
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Okabe A, Kaneda A. Hi-C Analysis to Identify Genome-Wide Chromatin Structural Aberration in Cancer. Methods Mol Biol 2023; 2519:127-140. [PMID: 36066718 DOI: 10.1007/978-1-0716-2433-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hi-C is a method that analyzes genome-wide chromatin structure using next-generation sequencer. Chromatin structure is crucial for regulating transcription or replication, and Hi-C has revealed the hierarchical chromatin structures, such as loop, domain , and compartment structures. Aberrant alteration of these structures causes disease, and a number of structural aberrations in cancer cells have been reported recently. Besides, Hi-C can identify chromosome rearrangements that frequently occurred in cancer. Therefore, Hi-C is a powerful technique to analyze epigenomic and genomic aberrations in tumorigenesis. Here we will introduce the basic protocol of Hi-C in experimental and analytical aspects.
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Affiliation(s)
- Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.
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20
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Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
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Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
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21
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Ding T, Zhang H. Novel biological insights revealed from the investigation of multiscale genome architecture. Comput Struct Biotechnol J 2022; 21:312-325. [PMID: 36582436 PMCID: PMC9791078 DOI: 10.1016/j.csbj.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gene expression and cell fate determination require precise and coordinated epigenetic regulation. The complex three-dimensional (3D) genome organization plays a critical role in transcription in myriad biological processes. A wide range of architectural features of the 3D genome, including chromatin loops, topologically associated domains (TADs), chromatin compartments, and phase separation, together regulate the chromatin state and transcriptional activity at multiple levels. With the help of 3D genome informatics, recent biochemistry and imaging approaches based on different strategies have revealed functional interactions among biomacromolecules, even at the single-cell level. Here, we review the occurrence, mechanistic basis, and functional implications of dynamic genome organization, and outline recent experimental and computational approaches for profiling multiscale genome architecture to provide robust tools for studying the 3D genome.
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Affiliation(s)
| | - He Zhang
- Corresponding author at: School of Life Science and Technology, Tongji University, Shanghai 200092, PR China.
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22
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Shao D, Yang Y, Shi S, Tong H. Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments. Genes (Basel) 2022; 13:genes13122317. [PMID: 36553584 PMCID: PMC9778438 DOI: 10.3390/genes13122317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.
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Affiliation(s)
- Dan Shao
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Yu Yang
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence: (Y.Y.); (S.S.)
| | - Shourong Shi
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
- Correspondence: (Y.Y.); (S.S.)
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
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23
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Feng Y, Wang P, Cai L, Zhan M, He F, Wang J, Li Y, Gega E, Zhang W, Zhao W, Xin Y, Chen X, Ruan Y, Lu L. 3D-Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100010. [PMID: 36911294 PMCID: PMC9993472 DOI: 10.1002/ggn2.202100010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 05/03/2022] [Indexed: 11/10/2022]
Abstract
The fundamental cause of transcription dysregulation in hepatocellular carcinoma (HCC) remains elusive. To investigate the underlying mechanisms, comprehensive 3D-epigenomic analyses are performed in cellular models of THLE2 (a normal hepatocytes cell line) and HepG2 (a hepatocellular carcinoma cell line) using integrative approaches for chromatin topology, genomic and epigenomic variation, and transcriptional output. Comparing the 3D-epigenomes in THLE2 and HepG2 reveal that most HCC-associated genes are organized in complex chromatin interactions mediated by RNA polymerase II (RNAPII). Incorporation of genome-wide association studies (GWAS) data enables the identification of non-coding genetic variants that are enriched in distal enhancers connecting to the promoters of HCC-associated genes via long-range chromatin interactions, highlighting their functional roles. Interestingly, CTCF binding and looping proximal to HCC-associated genes appear to form chromatin architectures that overarch RNAPII-mediated chromatin interactions. It is further demonstrated that epigenetic variants by DNA hypomethylation at a subset of CTCF motifs proximal to HCC-associated genes can modify chromatin topological configuration, which in turn alter RNAPII-mediated chromatin interactions and lead to dysregulation of transcription. Together, the 3D-epigenomic analyses provide novel insights of multifaceted interplays involving genetics, epigenetics, and chromatin topology in HCC cells.
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Affiliation(s)
- Yuliang Feng
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China.,The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Meixiao Zhan
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Fan He
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Yong Li
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Eva Gega
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Wei Zhang
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Wei Zhao
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Yongjie Xin
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Xudong Chen
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ligong Lu
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
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24
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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25
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Disney-Hogg L, Kinnersley B, Houlston R. Algorithmic considerations when analysing capture Hi-C data. Wellcome Open Res 2022; 5:289. [DOI: 10.12688/wellcomeopenres.16394.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
Abstract
Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promoter capture Hi-C data generated on 28 different cell lines as a case study.
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26
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Genomic, transcriptomic, and epigenomic analysis of a medicinal snake, Bungarus multicinctus, to provides insights into the origin of Elapidae neurotoxins. Acta Pharm Sin B 2022; 13:2234-2249. [DOI: 10.1016/j.apsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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27
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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28
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Wang X, Yan J, Ye Z, Zhang Z, Wang S, Hao S, Shen B, Wei G. Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells. Front Cell Dev Biol 2022; 10:974750. [PMID: 36003143 PMCID: PMC9393755 DOI: 10.3389/fcell.2022.974750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Doxorubicin resistance remains a major therapeutic challenge leading to poor survival prognosis and treatment failure in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape are well known, potential diagnostic or therapeutic targets associated with the reorganization of three-dimensional (3D) chromatin architecture have not yet been systematically investigated. Methods: Here we performed in situ high-throughput chromosome conformation capture (Hi-C) on parental and doxorubicin-resistant MCF7 (MCF7-DR) human breast cancer cells, followed by integrative analysis of HiC, ATAC-seq, RNA-seq and TCGA data. Results: It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression. The genome of MCF7-DR cells was spatially reorganized into smaller topologically associating domains (TADs) and chromatin loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF, AP-1 and bHLH, to gained TADs or loops. Intriguingly, we observed two condensed genomic regions (∼20 kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Finally, combining data from TCGA, we identified a number of gained and lost enhancer-promoter interactions and their corresponding differentially expressed genes involved in chromatin organization and breast cancer signaling pathways, including FA2H, FOXA1 and JRKL, which might serve as potential treatment targets for breast cancer. Conclusion: These data uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription and provide novel insights into the epigenomic mechanisms involving doxorubicin resistance in breast cancer.
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Affiliation(s)
- Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jizhou Yan
- Department of Developmental Biology, Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China
| | - Zhao Ye
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Zhang
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Sheng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuang Hao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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29
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Rico D, Kent D, Karataraki N, Mikulasova A, Berlinguer-Palmini R, Walker BA, Javierre BM, Russell LJ, Brackley CA. High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation. Genome Res 2022; 32:1355-1366. [PMID: 35863900 PMCID: PMC9341513 DOI: 10.1101/gr.276028.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
Genomic rearrangements are known to result in proto-oncogene deregulation in many cancers, but the link to 3D genome structure remains poorly understood. Here, we used the highly predictive heteromorphic polymer (HiP-HoP) model to predict chromatin conformations at the proto-oncogene CCND1 in healthy and malignant B cells. After confirming that the model gives good predictions of Hi-C data for the nonmalignant human B cell-derived cell line GM12878, we generated predictions for two cancer cell lines, U266 and Z-138. These possess genome rearrangements involving CCND1 and the immunoglobulin heavy locus (IGH), which we mapped using targeted genome sequencing. Our simulations showed that a rearrangement in U266 cells where a single IGH super-enhancer is inserted next to CCND1 leaves the local topologically associated domain (TAD) structure intact. We also observed extensive changes in enhancer-promoter interactions within the TAD, suggesting that it is the downstream chromatin remodeling which gives rise to the oncogene activation, rather than the presence of the inserted super-enhancer DNA sequence per se. Simulations of the IGH-CCND1 reciprocal translocation in Z-138 cells revealed that an oncogenic fusion TAD is created, encompassing CCND1 and the IGH super-enhancers. We predicted how the structure and expression of CCND1 changes in these different cell lines, validating this using qPCR and fluorescence in situ hybridization microscopy. Our work demonstrates the power of polymer simulations to predict differences in chromatin interactions and gene expression for different translocation breakpoints.
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Affiliation(s)
- Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Kent
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nefeli Karataraki
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana 46202, USA
| | - Biola M Javierre
- Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, 08916 Badalona, Barcelona, Spain
| | - Lisa J Russell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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30
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Wu Z, Wang L, Fan L, Tang H, Zuo X, Gu D, Lu X, Li Y, Wu J, Qin S, Xia Y, Zhu H, Wang L, Xu W, Li J, Jin H. Exploring the significance of PAK1 through chromosome conformation signatures in ibrutinib-resistant chronic lymphocytic leukaemia. Mol Oncol 2022; 16:2920-2935. [PMID: 35811334 PMCID: PMC9394240 DOI: 10.1002/1878-0261.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Ibrutinib exerts promising anticancer effects in chronic lymphocytic leukaemia (CLL). However, acquired resistance occurs during treatment, necessitating the exploration of underlying mechanisms. Although three‐dimensional genome organization has been identified as a major player in the development and progression of cancer, including drug resistance, little is known regarding its role in CLL. Therefore, we investigated the molecular mechanisms underlying ibrutinib resistance through multi‐omics analysis, including high‐throughput chromosome conformation capture (Hi‐C) technology. We demonstrated that the therapeutic response to ibrutinib is associated with the expression of p21‐activated kinase 1 (PAK1). PAK1, which was up‐regulated in CLL and associated with patients' survival, was involved in cell proliferation, glycolysis and oxidative phosphorylation. Furthermore, the PAK1 inhibitor IPA‐3 exerted an anti‐tumour effect and its combination with ibrutinib exhibited a synergistic effect in ibrutinib‐sensitive and ‐resistant cells. These findings suggest the oncogenic role of PAK1 in CLL progression and drug resistance, highlighting PAK1 as a potential diagnostic marker and therapeutic target in CLL including ibrutinib‐resistant CLL.
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Affiliation(s)
- Zijuan Wu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Luqiao Wang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Lei Fan
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Hanning Tang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Xiaoling Zuo
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Danling Gu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Xueying Lu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Yue Li
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Jiazhu Wu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Shuchao Qin
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Yi Xia
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Huayuan Zhu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Li Wang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Wei Xu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Jianyong Li
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China.,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui Jin
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China.,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
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31
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Peng A, Peng W, Wang R, Zhao H, Yu X, Sun Y. Regulation of 3D Organization and Its Role in Cancer Biology. Front Cell Dev Biol 2022; 10:879465. [PMID: 35757006 PMCID: PMC9213882 DOI: 10.3389/fcell.2022.879465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Three-dimensional (3D) genomics is the frontier field in the post-genomics era, its foremost content is the relationship between chromatin spatial conformation and regulation of gene transcription. Cancer biology is a complex system resulting from genetic alterations in key tumor oncogenes and suppressor genes for cell proliferation, DNA replication, cell differentiation, and homeostatic functions. Although scientific research in recent decades has revealed how the genome sequence is mutated in many cancers, high-order chromosomal structures involved in the development and fate of cancer cells represent a crucial but rarely explored aspect of cancer genomics. Hence, dissection of the 3D genome conformation of cancer helps understand the unique epigenetic patterns and gene regulation processes that distinguish cancer biology from normal physiological states. In recent years, research in tumor 3D genomics has grown quickly. With the rapid progress of 3D genomics technology, we can now better determine the relationship between cancer pathogenesis and the chromatin structure of cancer cells. It is becoming increasingly explicit that changes in 3D chromatin structure play a vital role in controlling oncogene transcription. This review focuses on the relationships between tumor gene expression regulation, tumor 3D chromatin structure, and cancer phenotypic plasticity. Furthermore, based on the functional consequences of spatial disorganization in the cancer genome, we look forward to the clinical application prospects of 3D genomic biomarkers.
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Affiliation(s)
- Anghui Peng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Wang Peng
- Department of Oncology, Liuzhou People's Hospital, Liuzhou, China
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Hao Zhao
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xinyang Yu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yihao Sun
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
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32
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Du Y, Gu Z, Li Z, Yuan Z, Zhao Y, Zheng X, Bo X, Chen H, Wang C. Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200818. [PMID: 35570408 PMCID: PMC9218654 DOI: 10.1002/advs.202200818] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/04/2022] [Indexed: 06/05/2023]
Abstract
Structural variations (SVs) are the greatest source of variations in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human cancer remain technologically challenging. Here, long-read sequencing is first employed to depict the signatures of structural variations in carcinogenesis of human pancreatic ductal epithelium. Then widespread reprogramming of the 3D chromatin architecture is revealed by an in situ Hi-C technique. Integrative analyses indicate that the distribution pattern of SVs among the 3D genome is highly cell-type specific and the bulk remodeling effects of SVs in the chromatin organization partly depend on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability. Notably, complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4 are identified, and their influence on the expression of oncogenes MIR31HG, MYO5B, etc., are further elucidated from both a linear view and 3D perspective. Overall, this work provides a genome-wide resource and highlights the impact, complexity, and dynamicity of the interplay between structural variations and high-order chromatin organization, which expands the current understanding of the pathogenesis of SVs in human cancer.
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Affiliation(s)
- Yongxing Du
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zongting Gu
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zongze Li
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zan Yuan
- Annoroad Gene Technology Co. LtdBeijing100176P. R. China
| | - Yue Zhao
- Annoroad Gene Technology Co. LtdBeijing100176P. R. China
| | - Xiaohao Zheng
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiaochen Bo
- Department of BiotechnologyInstitute of Health Service and Transfusion MedicineBeijing100850P. R. China
| | - Hebing Chen
- Department of BiotechnologyInstitute of Health Service and Transfusion MedicineBeijing100850P. R. China
| | - Chengfeng Wang
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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33
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Ashby C, Boyle EM, Bauer MA, Mikulasova A, Wardell CP, Williams L, Siegel A, Blaney P, Braunstein M, Kaminetsky D, Keats J, Maura F, Landgren O, Walker BA, Davies FE, Morgan GJ. Structural variants shape the genomic landscape and clinical outcome of multiple myeloma. Blood Cancer J 2022; 12:85. [PMID: 35637217 PMCID: PMC9151656 DOI: 10.1038/s41408-022-00673-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/11/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Deciphering genomic architecture is key to identifying novel disease drivers and understanding the mechanisms underlying myeloma initiation and progression. In this work, using the CoMMpass dataset, we show that structural variants (SV) occur in a nonrandom fashion throughout the genome with an increased frequency in the t(4;14), RB1, or TP53 mutated cases and reduced frequency in t(11;14) cases. By mapping sites of chromosomal rearrangements to topologically associated domains and identifying significantly upregulated genes by RNAseq we identify both predicted and novel putative driver genes. These data highlight the heterogeneity of transcriptional dysregulation occurring as a consequence of both the canonical and novel structural variants. Further, it shows that the complex rearrangements chromoplexy, chromothripsis and templated insertions are common in MM with each variant having its own distinct frequency and impact on clinical outcome. Chromothripsis is associated with a significant independent negative impact on clinical outcome in newly diagnosed cases consistent with its use alongside other clinical and genetic risk factors to identify prognosis.
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Affiliation(s)
- Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Michael A Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Aneta Mikulasova
- Institute of Cellular Medicine, University of Newcastle upon Tyne, Newcastle, UK
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Louis Williams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ariel Siegel
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Marc Braunstein
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Jonathan Keats
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, USA
| | | | - Ola Landgren
- Sylvester Cancer Center University of Miami, Miami, FL, USA
| | - Brian A Walker
- Division of Hematology Oncology Indiana University, Indianapolis, IN, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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34
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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35
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Comparative characterization of 3D chromatin organization in triple-negative breast cancers. Exp Mol Med 2022; 54:585-600. [PMID: 35513575 PMCID: PMC9166756 DOI: 10.1038/s12276-022-00768-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a malignant cancer subtype with a high risk of recurrence and an aggressive phenotype compared to other breast cancer subtypes. Although many breast cancer studies conducted to date have investigated genetic variations and differential target gene expression, how 3D chromatin architectures are reorganized in TNBC has been poorly elucidated. Here, using in situ Hi-C technology, we characterized the 3D chromatin organization in cells representing five distinct subtypes of breast cancer (including TNBC) compared to that in normal cells. We found that the global and local 3D architectures were severely disrupted in breast cancer. TNBC cell lines (especially BT549 cells) showed the most dramatic changes relative to normal cells. Importantly, we detected CTCF-dependent TNBC-susceptible losses/gains of 3D chromatin organization and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulation. In TNBC tissue, 3D chromatin disorganization was also observed relative to the 3D chromatin organization in normal tissues. We observed that the perturbed local 3D architectures found in TNBC cells were partially conserved in TNBC tissues. Finally, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. In this study, we elucidated the characteristics of the 3D chromatin organization in breast cancer relative to normal cells/tissues at multiple scales and identified associations between disrupted structures and various epigenetic features and transcriptomes. Collectively, our findings reveal important 3D chromatin structural features for future diagnostic and therapeutic studies of TNBC. The 3D architecture of the genome is dramatically altered in an aggressive form of breast cancer, leading to changes in the regulation of gene expression that can fuel tumor growth. A team from South Korea, led by Hyeong-Gon Moon of Seoul National University College of Medicine and Daeyoup Lee of the Korea Advanced Institute of Science and Technology, Daejeon, detailed how chromosomes are positioned and folded within the nucleus of cell liness from five different subtypes of breast cancer. They found that triple-negative breast cancers displayed the most extreme reorganization of their genomes, a pattern also observed in biopsy tissues taken from patients with this subtype of cancer. Knowledge of these conformational changes could inform future efforts to develop therapies and diagnostics for patients with triple-negative breast tumors.
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36
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Trasanidis N, Katsarou A, Ponnusamy K, Shen YA, Kostopoulos IV, Bergonia B, Keren K, Reema P, Xiao X, Szydlo RM, Sabbattini PMR, Roberts IAG, Auner HW, Naresh KN, Chaidos A, Wang TL, Magnani L, Caputo VS, Karadimitris A. Systems medicine dissection of chr1q-amp reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma. Blood 2022; 139:1939-1953. [PMID: 35015835 DOI: 10.1182/blood.2021014391] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding the biological and clinical impact of copy number aberrations (CNAs) on the development of precision therapies in cancer remains an unmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNA conferring an adverse prognosis in several types of cancer, including in the blood cancer multiple myeloma (MM). Although several genes across chromosome 1 (chr1q) portend high-risk MM disease, the underpinning molecular etiology remains elusive. Here, with reference to the 3-dimensional (3D) chromatin structure, we integrate multi-omics data sets from patients with MM with genetic variables to obtain an associated clinical risk map across chr1q and to identify 103 adverse prognosis genes in chr1q-amp MM. Prominent among these genes, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed superenhancers, PBX1 directly regulates critical oncogenic pathways and a FOXM1-dependent transcriptional program. Together, PBX1 and FOXM1 activate a proliferative gene signature that predicts adverse prognosis across multiple types of cancer. Notably, pharmacological disruption of the PBX1-FOXM1 axis with existing agents (thiostrepton) and a novel PBX1 small molecule inhibitor (T417) is selectively toxic against chr1q-amp myeloma and solid tumor cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes, and proposes novel CNA-targeted therapy strategies in MM and other types of cancer.
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Affiliation(s)
- Nikolaos Trasanidis
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alexia Katsarou
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kanagaraju Ponnusamy
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yao-An Shen
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ioannis V Kostopoulos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Bien Bergonia
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Keren Keren
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Paudel Reema
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Xiaolin Xiao
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Richard M Szydlo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Pierangela M R Sabbattini
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Irene A G Roberts
- Department of Paediatrics and Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
- Oxford Biomedical Research Centre Blood Theme, National Institute for Health Research Oxford Biomedical Centre, Oxford, United Kingdom
| | - Holger W Auner
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kikkeri N Naresh
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Aristeidis Chaidos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Tian-Li Wang
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom; and
| | - Valentina S Caputo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Cancer Biology and Therapy Laboratory, School of Applied Science, London South Bank University, London, United Kingdom
| | - Anastasios Karadimitris
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
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37
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Agent myeloma has a new weapon from (ch1)Q. Blood 2022; 139:1927-1928. [PMID: 35357482 DOI: 10.1182/blood.2021015336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 11/20/2022] Open
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38
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Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nat Commun 2021; 12:6858. [PMID: 34824214 PMCID: PMC8617201 DOI: 10.1038/s41467-021-27091-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023] Open
Abstract
Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs' recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.
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39
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Guo D, Xie Q, Jiang S, Xie T, Li Y, Huang X, Li F, Wang T, Sun J, Wang A, Zhang Z, Li H, Bo X, Chen H, Liang Z. Synergistic alterations in the multilevel chromatin structure anchor dysregulated genes in small cell lung cancer. Comput Struct Biotechnol J 2021; 19:5946-5959. [PMID: 34849199 PMCID: PMC8604672 DOI: 10.1016/j.csbj.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive form of lung cancer that uniquely changes the chromosomal structure, although the basis of aberrant gene expression in SCLC remains largely unclear. Topologically associated domains (TADs) are structural and functional units of the human genome. Genetic and epigenetic alterations in the cancer genome can lead to the disruption of TAD boundaries and may cause gene dysregulation. To understand the potential regulatory role of this process in SCLC, we developed the TAD boundary alteration-related gene identification in tumors (TARGET) computational framework, which enables the systematic identification of candidate dysregulated genes associated with altered TAD boundaries. Using TARGET to compare gene expression profiles between SCLC and normal human lung fibroblast cell lines, we identified >100 genes in this category, of which 24 were further verified in samples from patients with SCLC using NanoString. The analysis revealed synergistic chromatin structure alteration at the A/B compartment and TAD boundary levels that underlies aberrant gene expression in SCLC. TARGET is a novel and powerful tool that can be used to explore the relationship of chromatin structure alteration to gene dysregulation related to SCLC tumorigenesis, progression, and prognosis.
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Affiliation(s)
- Dan Guo
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Qiu Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Shuai Jiang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ting Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yaru Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fangyuan Li
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tingting Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jian Sun
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Anqi Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zixin Zhang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hao Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hebing Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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40
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Aboelnour E, Bonev B. Evolutionary conservation and cell type specificity of nuclear compartments in the brain. Trends Neurosci 2021; 45:3-5. [PMID: 34756461 DOI: 10.1016/j.tins.2021.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 10/20/2022]
Abstract
In the cell nucleus, radial genome organization relative to the nuclear lamina exhibits both cell type-specific variability and evolutionarily conserved distribution. A recent study by Ahanger, Delgado et al. explores the in vivo spatial distribution of the genome in the brain and identifies conserved genomic localization across mammalian species that are correlated with gene expression states.
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Affiliation(s)
- Erin Aboelnour
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; Physiological Genomics, Biomedical Center, Ludwig Maximilian University, Munich, Germany.
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Xu L, Yin L, Qi Y, Tan X, Gao M, Peng J. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing. Acta Pharm Sin B 2021; 11:3150-3164. [PMID: 34729306 PMCID: PMC8546856 DOI: 10.1016/j.apsb.2021.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/30/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular function and physiological processes. High-throughput chromosome conformation capture (Hi-C), Nanopore sequencing, and RNA-sequencing (RNA-seq) assays were performed on the liver of normal and NAFLD mice. A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops by Hi-C, and whole genome sequencing identifying structural variations (SVs) and copy number variations (CNVs) by Nanopore sequencing. We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements, between normal and NAFLD mice, and revealed gene dysregulation frequently accompanied by these variations. Candidate target genes were identified in NAFLD, impacted by genetic rearrangements and spatial organization disruption. Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations, revealed the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD. The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.
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Key Words
- 3C, chromosome conformation capture
- 3D genome
- 3D, three-dimensional
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- Abcg5, ATP-binding cassette sub-family G member 5
- BWA, Burrows-Wheeler Aligner
- CNV, copy number variation
- Camk1d, calcium/calmodulin-dependent protein kinase type 1D
- Chr, chromosome
- Chromatin looping
- DEG, differentially expressed gene
- DEL, deletion
- DI, directionality index
- DUP, duplication
- Elovl6, elongation of very long chain fatty acids protein 6
- FDR, false discovery rate
- FFA, free fatty acid
- Fgfr2, fibroblast growth factor receptor 2
- GCKR, glucokinase regulator
- GO, gene ontology
- GSH, glutathione
- Gadd45g, growth arrest and DNA damage-inducible protein GADD45 gamma
- Grm8, metabotropic glutamate receptor 8
- Gsta1, glutathione S-transferase A1
- H&E, hematoxylin-eosin
- HFD, high-fat diet
- HSD17B13, hydroxysteroid 17-beta dehydrogenase 13
- Hi-C, high-throughput chromosome conformation capture
- IDE, interaction decay exponent
- INS, insertion
- INV, inversion
- IR, inclusion ratio
- IRGM, immunity related GTPase M
- IRS4, insulin receptor substrate 4
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Kcnma1, calcium-activated potassium channel subunit alpha-1
- LPIN1, lipin 1
- MBOAT7, membrane bound O-acyltransferase domain containing 7
- MDA, malondialdehyde
- NAFLD, non-alcoholic fatty liver disease
- NF1, neurofibromin 1
- NGS, next-generation sequencing
- NOTCH1, notch receptor 1
- ONT, Oxford Nanopore Technologies
- PCA, principal component analysis
- PNPLA3, patatin like phospholipase domain containing 3
- PPP1R3B, protein phosphatase 1 regulatory subunit 3B
- PTEN, phosphatase and tensin homolog
- Pde4b, phosphodiesterase 4B
- Plce1, 1-phosphat-idylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
- Plxnb1, Plexin-B1
- RB1, RB transcriptional corepressor 1
- RNA-seq, RNA-sequencing
- SD, standard deviation
- SOD, superoxide dismutase
- SV, structural variation
- Scd1, acyl-CoA desaturase 1
- Sugct, succinate-hydroxymethylglutarate CoA-transferase
- TAD, topologically associated domain
- TC, total cholesterol
- TG, triglyceride
- TM6SF2, transmembrane 6 superfamily member 2
- TP53, tumor protein p53
- TRA, translocation
- Topologically associated domain
- Transcriptome
- WGS, whole-genome sequencing
- Whole-genome sequencing
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Danieli A, Papantonis A. Spatial genome architecture and the emergence of malignancy. Hum Mol Genet 2021; 29:R197-R204. [PMID: 32619215 DOI: 10.1093/hmg/ddaa128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter-enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.
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Affiliation(s)
- Adi Danieli
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
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Derrien J, Guérin-Charbonnel C, Gaborit V, Campion L, Devic M, Douillard E, Roi N, Avet-Loiseau H, Decaux O, Facon T, Mallm JP, Eils R, Munshi NC, Moreau P, Herrmann C, Magrangeas F, Minvielle S. The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability. Genome Med 2021; 13:127. [PMID: 34372935 PMCID: PMC8351364 DOI: 10.1186/s13073-021-00938-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective. METHODS Here, we performed an analysis of 42 MM samples from 21 patients by using enhanced reduced representation bisulfite sequencing (eRRBS). We combined several metrics of epigenetic heterogeneity to analyze DNA methylation heterogeneity in MM patients. RESULTS We show that MM is characterized by the continuous accumulation of stochastic methylation at the promoters of development-related genes. High combinatorial entropy change is associated with poor outcomes in our pilot study and depends predominantly on partially methylated domains (PMDs). These PMDs, which represent the major source of inter- and intrapatient DNA methylation heterogeneity in MM, are linked to other key epigenetic aberrations, such as CpG island (CGI)/transcription start site (TSS) hypermethylation and H3K27me3 redistribution as well as 3D organization alterations. In addition, transcriptome analysis revealed that intratumor methylation heterogeneity was associated with low-level expression and high variability. CONCLUSIONS We propose that disrupted DNA methylation in MM is responsible for high epigenetic and transcriptomic instability allowing tumor cells to adapt to environmental changes by tapping into a pool of evolutionary trajectories.
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Affiliation(s)
- Jennifer Derrien
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
| | - Catherine Guérin-Charbonnel
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Institut de Cancérologie de l'Ouest, Nantes-Saint Herblain, France
| | - Victor Gaborit
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- LS2N, CNRS, Université de Nantes, Nantes, France
| | - Loïc Campion
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Institut de Cancérologie de l'Ouest, Nantes-Saint Herblain, France
| | - Magali Devic
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Elise Douillard
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Nathalie Roi
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Hervé Avet-Loiseau
- Institut Universitaire du Cancer, CHU, Centre de Recherche en Cancérologie de Toulouse, INSERM 1037, Toulouse, France
| | | | | | - Jan-Philipp Mallm
- Research Group Genome Organization & Function, DKFZ, and BioQuant Heidelberg, Heidelberg, 69120, Germany
| | - Roland Eils
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, 69120, Germany
- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt- Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
- Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, Berlin, 10178, Germany
| | - Nikhil C Munshi
- Dana-Farber Cancer Institute, Harvard Medical School, LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Boston, MA, United States
| | - Philippe Moreau
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, 69120, Germany
| | - Florence Magrangeas
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Stéphane Minvielle
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.
- Centre Hospitalier Universitaire, Nantes, France.
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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45
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Adeel MM, Jiang H, Arega Y, Cao K, Lin D, Cao C, Cao G, Wu P, Li G. Structural Variations of the 3D Genome Architecture in Cervical Cancer Development. Front Cell Dev Biol 2021; 9:706375. [PMID: 34368157 PMCID: PMC8344058 DOI: 10.3389/fcell.2021.706375] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022] Open
Abstract
Human papillomavirus (HPV) integration is the major contributor to cervical cancer (CC) development by inducing structural variations (SVs) in the human genome. SVs are directly associated with the three-dimensional (3D) genome structure leading to cancer development. The detection of SVs is not a trivial task, and several genome-wide techniques have greatly helped in the identification of SVs in the cancerous genome. However, in cervical cancer, precise prediction of SVs mainly translocations and their effects on 3D-genome and gene expression still need to be explored. Here, we have used high-throughput chromosome conformation capture (Hi-C) data of cervical cancer to detect the SVs, especially the translocations, and validated it through whole-genome sequencing (WGS) data. We found that the cervical cancer 3D-genome architecture rearranges itself as compared to that in the normal tissue, and 24% of the total genome switches their A/B compartments. Moreover, translocation detection from Hi-C data showed the presence of high-resolution t(4;7) (q13.1; q31.32) and t(1;16) (q21.2; q22.1) translocations, which disrupted the expression of the genes located at and nearby positions. Enrichment analysis suggested that the disrupted genes were mainly involved in controlling cervical cancer-related pathways. In summary, we detect the novel SVs through Hi-C data and unfold the association among genome-reorganization, translocations, and gene expression regulation. The results help understand the underlying pathogenicity mechanism of SVs in cervical cancer development and identify the targeted therapeutics against cervical cancer.
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Affiliation(s)
- Muhammad Muzammal Adeel
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hao Jiang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yibeltal Arega
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Kai Cao
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Peng Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
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46
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Wang Y, An G, Qiu LG. [Progress in clonal evolution of multiple myeloma]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:611-615. [PMID: 34455753 PMCID: PMC8408495 DOI: 10.3760/cma.j.issn.0253-2727.2021.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Y Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - G An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - L G Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
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Li Y, Xue B, Zhang M, Zhang L, Hou Y, Qin Y, Long H, Su QP, Wang Y, Guan X, Jin Y, Cao Y, Li G, Sun Y. Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency. Genome Biol 2021; 22:206. [PMID: 34253239 PMCID: PMC8276456 DOI: 10.1186/s13059-021-02424-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/30/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. RESULTS We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. CONCLUSION Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.
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Affiliation(s)
- Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Guan
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yanyan Jin
- Department of Neurobiology, Beijing Centre of Neural Regeneration and Repair, Capital Medical University, Beijing, 100101, China
| | - Yuan Cao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
- College of Future Technology, Peking University, Beijing, 100871, China.
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48
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Zhang X, Liu X, Du Z, Wei L, Fang H, Dong Q, Niu J, Li Y, Gao J, Zhang MQ, Xie W, Wang X. The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. Genome Res 2021; 31:1121-1135. [PMID: 34140314 PMCID: PMC8256869 DOI: 10.1101/gr.275235.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023]
Abstract
Heterochromatin remodeling is critical for various cell processes. In particular, the "loss of heterochromatin" phenotype in cellular senescence is associated with the process of aging and age-related disorders. Although biological processes of senescent cells, including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction, and redistribution of key proteins, have been closely associated with high-order chromatin structure, the relationship between the high-order chromatin reorganization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and deep senescent fibroblasts induced by DNA damage harboring the "loss of heterochromatin" phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, show different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Both types of heterochromatin show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show both similar and distinct multiscale alterations in the 3D map, chromatin accessibility, and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.
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Affiliation(s)
- Xianglin Zhang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Xuehui Liu
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
- State Key Laboratory of Medical Molecular Biology, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Huan Fang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Qiongye Dong
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Jing Niu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanda Li
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Michael Q Zhang
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Richardson, Texas 75080-3021, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
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49
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Li T, Li R, Dong X, Shi L, Lin M, Peng T, Wu P, Liu Y, Li X, He X, Han X, Kang B, Wang Y, Liu Z, Chen Q, Shen Y, Feng M, Wang X, Wu D, Wang J, Li C. Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:741-753. [PMID: 34116262 PMCID: PMC9170781 DOI: 10.1016/j.gpb.2020.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/28/2020] [Accepted: 06/11/2020] [Indexed: 10/31/2022]
Abstract
Genomic studies of cancer cell alterations, such as mutations, copy number variations (CNVs), and translocations, greatly promote our understanding of the genesis and development of cancer. However, the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical difficulties. To explore the 3D genome structure in clinical lung cancer, we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer, combining with RNA-seq analysis. We demonstrated the feasibility of studying 3D genome of clinical lung cancer samples with a small number of cells (1 × 104), compared the genome architecture between clinical samples and cell lines of lung cancer, and identified conserved and changed spatial chromatin structures between normal and cancer samples. We also showed that Hi-C data can be used to infer CNVs and point mutations in cancer. By integrating those different types of cancer alterations, we showed significant associations between CNVs, 3D genome, and gene expression. We propose that 3D genome mediates the effects of cancer genomic alterations on gene expression through altering regulatory chromatin structures. Our study highlights the importance of analyzing 3D genomes of clinical cancer samples in addition to cancer cell lines and provides an integrative genomic analysis pipeline for future larger-scale studies in lung cancer and other cancers.
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Affiliation(s)
- Tingting Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China; State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Ruifeng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Lin Shi
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai 200433, China; Fudan University Center for Clinical Bioinformatics, Shanghai 200433, China
| | - Miao Lin
- Department of Thoracic Surgery, Zhongshan Hospital of Fudan University, Shanghai 200032, China
| | - Ting Peng
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Pengze Wu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuting Liu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Xiaoting Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuheng He
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xu Han
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Bin Kang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yinan Wang
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Zhiheng Liu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Qing Chen
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China; BGI-Qingdao, Qingdao 266426, China; Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mingxiang Feng
- Department of Thoracic Surgery, Zhongshan Hospital of Fudan University, Shanghai 200032, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai 200433, China; Fudan University Center for Clinical Bioinformatics, Shanghai 200433, China
| | - Duojiao Wu
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai 200433, China.
| | - Jian Wang
- iCarbonX, Shenzhen 518053, China; Digital Life Research Institute, Shenzhen 518110, China.
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China.
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Scourzic L, Salataj E, Apostolou E. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Front Immunol 2021; 12:669881. [PMID: 34054841 PMCID: PMC8160312 DOI: 10.3389/fimmu.2021.669881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B/T lymphocytes. Finally, we present how alterations in architectural factors and/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.
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Affiliation(s)
| | | | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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